Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103136
Name   oriT_pCfr-30 in_silico
Organism   Citrobacter freundii strain 30
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY659387 (48521..49138 [+], 618 nt)
oriT length   618 nt
IRs (inverted repeats)      589..594, 608..613  (TCCATG..CATGGA)
 592..597, 602..607  (ATGCCC..GGGCAT)
 520..527, 530..537  (CCTCCCGT..ACGGGAGG)
 455..460, 464..469  (ATTCGC..GCGAAT)
 197..202, 208..213  (TTCAAT..ATTGAA)
 85..90, 96..101  (TGCTTT..AAAGCA)
Location of nic site      315..316
Conserved sequence flanking the
  nic site    		  TCCTGCATCG
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 618 nt

>oriT_pCfr-30
TTCTTTGTTTCCCTGTCAAATACATTGTGGTTTTGATAAAATCATCATTGTCTTTTGACACATTAACATCTTCATTTTTAACCTTGCTTTTCAGTAAAGCATTGGCAAGCAGCTTCATTCCTTTTGCCACGGTTAAACCCGGTTCATCTGGATAAAGTGTTTTAAGACAATCAAGTAGATCATCATGTTGGCTTTCTTCAATCCTGAATTGAACTTTTTTCATAAAACTCTCCAACAAGAACCGACTGTAGGTCACCGGGCAAACGTTGCGGAATGGCGTCAGAGACGTCATTTTGCGGCGTTTGCCCTATCCTGCATCGCAGTGAACTACCTCCACACATAAATTGTGCTTCAGCGTCCATCGAAATGCAAAAAATGAAAGGCTATCGTGGCTGTGATCTGGTGCGTCTGCGACCGGAGACAACGGATTCGCGGCTAACTTGGGCGGAAATAAATTCGCTACGCGAATGGCCTGGCAGGGGGCGCGAGCGCTGTTTTACGGAATATACAAAAAAAGCACCTCCCGTAAACGGGAGGGCTTCGGCGATTCAGGAACGGGAATTTTATTCTGCCTCTGGTGTGTCGCCTTCCATGCCCTGCCGGGCATCATGGAGCCAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2352 GenBank   WP_004199101
Name   Relaxase_HTM42_RS00255_pCfr-30 insolico UniProt ID   A0A515HL38
Length   386 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 386 a.a.        Molecular weight: 44388.82 Da        Isoelectric Point: 10.6017

>WP_004199101.1 MULTISPECIES: MobP1 family relaxase [Enterobacterales]
MGVYVDKEFRVKRKSSEAGRKSAFAHKVKNGGKNYQRNVQERINRKGASKEVVVKISGGAITRQGVRNSI
DYMSRESELPVMSESGQVWKGDEIQEAKEHMIDRANDPQNVFDDKGKENKKVTQNIVFSPPVSAKVKPED
LLESVRKTMNKKYPNHRFVLGYHNDKKEHPHVHVVFRIRDNDGKRADIRKKDLREIRTGFCEELKMKGYD
VKATHKQQHGLNQSIKDAHKTAPKRQKGVYEVVDVGYDHYQNDKTKPKQHFIKLKTLNKGVEKTYWGADF
GELTTRENVKKGDLVKLKKLGQKEVKIPALDKNGVQHGWKTAHRNEWQLENLGVKGIDRISSSSKELVLN
SAEMIKKQQLQMRNFSQIKQSMIQSEQKVKIGIRLG

  Protein domains


Predicted by InterproScan.

Relaxase/Mobilisation nuclease domain (Relaxase)

(90-240)


  Protein structure


Source ID Structure
AlphaFold DB A0A515HL38


T4CP

ID   2083 GenBank   WP_000053822
Name   t4cp2_HTM42_RS00185_pCfr-30 insolico UniProt ID   _
Length   611 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 611 a.a.        Molecular weight: 69204.04 Da        Isoelectric Point: 7.4342

>WP_000053822.1 MULTISPECIES: type IV secretory system conjugative DNA transfer family protein [Enterobacterales]
MSLKLPDKGQWAFIGLVMCLVTYYTGSVAVYFLNGKTPLYIWKNFDSMLLWRIITESNIRTDIRLTAIPS
LLSGMVSSLIVPVFIIWQLNKTDVALYGDAKFASDNDLRKSKLLKWEKENDTDILVGAYKGKYLWYTAPD
FVSLGAGTRAGKGAAIGIPNLLVRKHSLIALDPKQELWKITSKVREKLLGNKVYLLDPFNSKTHQFNPLF
YIDLKEESGAKDLLKLIEILFPSYGLTGAEAHFNNLAGQYWTGLAKLLHFFINYDPSWLGEFGLKPVFSI
GSVVDLYSNIDRELILSKREDLEGTKGLDENALYHLRDALTKIREYHETEDEQRSSIDGSFRKKMSLFYL
PTVRKCTDGNDFDLRQLRREDITVYVGVNAEDMSLAYDFLNLFFNFVVEVTLRENPDFDPTLKHDCLMFL
DEFPSIGYMPIIKKGSGYIAGFKLKLLTIYQNISQLNEIYGVEGAKTLMSAHPCRIIYAVSEEDDAKKIS
EKLGYITTKSTGSSKTSGRSTSKSSSESEAQRALVLPQELGTLDFKEEFIILKGENPVKAEKALYFLDPY
FMDRLMMVSPKLTELTASLNKTKKVLGVKGLKYPSKEKMLSVGELESEVLL

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(102-572)

  Protein structure



No available structure.



ID   2084 GenBank   WP_000108726
Name   t4cp2_HTM42_RS00230_pCfr-30 insolico UniProt ID   _
Length   917 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 917 a.a.        Molecular weight: 104822.73 Da        Isoelectric Point: 6.2666

>WP_000108726.1 MULTISPECIES: VirB3 family type IV secretion system protein [Enterobacterales]
MSTVFKGLTRPALIRGLGVPLYPFLGMCVICVLLGVWIHEAMYALILPGWYAIKRVTKIDERFFDLLYLR
MQIKGNPLANKRFNAVHYAGSSYDAVDISKVDNFMKLKDQSSLEELIPYSSHITDNLIVTRNHDLLATWQ
IDGAYFECVDEADLALLTDQLNTLIRSFDGKPVTFYTHRIRVRKEVRPVFDSKIPFVNRVMNDYYESLSA
AEYFENKLYLTVCYKPFSAEDKVTHFLSRKKGNKNIFEEPINDMNEICGRLSTYLSRFHSRRLGLYEENN
IVYSEQLTLFQKLLSGRWQKVRVTNSPFYTYLGGKDLFFGNDAGQITASDHARYFRCIEIKDYFQETDAG
IFDALMYLPVEYVQTSSFTPIDKQSAIKALDDQIDKLEMTDDAAKSLLADLKVGLDMVSSGYISFGKSHQ
TLIVYADSPERLVKDTNIVTTTLEDLGLIVTYSTLSLGAAYFAQLPGNYTLRPRLSSISSLNFAEMESFH
NFFTGKEKGNTWGNNLITLGGSGNDIYNLNYHMTTEHQNYFGKNPTLGHTEILGTSNVGKTVVMMTKAFA
AQQFGTPESFPPERKLKKLTTVFFDKDRAAEPGIRSMGGAYFRVKEGEPTGWNPAALPPTKRNISFMKDL
VRLLCTLNSEPLDDYQNRLISDAVERLMQRSNRSYPISKLRPLILEPDDTETRRHGLKARLNAWVQGGEF
GWVFDNPDDTFDVDNLDVFGIDGTEFLDNKVLSSAASFYLIYRVTMLADGRRLLIYMDEFWQWINNEAFR
DFVYNKLKTARKLDMVLVVATQSPDELIKSPIAAAVREQCATHIYLANPKAKRSEYVDELEVRELYFDKI
KAIDPLSRQFLVVKNPQRKGESDDFAAFARLDLGKAAYYLPVLSASKPQLELFDEIWKEGMKPEEWLDTY
LERANLI

  Protein domains


Predicted by InterproScan.

Type IV secretory pathway, VirB3-like protein (VirB3)

(2-83)

CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)

(272-474)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 35831..45940

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTM42_RS00160 30954..32216 - 1263 WP_000517490 ATP-binding protein -
HTM42_RS00165 32299..32793 - 495 WP_001215543 thermonuclease family protein -
HTM42_RS00170 32790..33116 - 327 WP_004208538 hypothetical protein -
HTM42_RS00175 33202..33516 - 315 WP_000754496 TrbM/KikA/MpfK family conjugal transfer protein -
HTM42_RS00180 33604..33996 - 393 WP_000738524 cag pathogenicity island Cag12 family protein -
HTM42_RS00185 33993..35828 - 1836 WP_000053822 type IV secretory system conjugative DNA transfer family protein -
HTM42_RS00190 35831..36865 - 1035 WP_000650512 P-type DNA transfer ATPase VirB11 virB11
HTM42_RS00195 36862..37059 - 198 WP_000629109 DNA-binding protein -
HTM42_RS00200 37061..38275 - 1215 WP_001295060 VirB10/TraB/TrbI family type IV secretion system protein virB10
HTM42_RS00205 38272..39201 - 930 WP_000783386 TrbG/VirB9 family P-type conjugative transfer protein virB9
HTM42_RS00210 39207..39935 - 729 WP_004199085 type IV secretion system protein virB8
HTM42_RS00215 40130..41185 - 1056 WP_000235886 type IV secretion system protein virB6
HTM42_RS00220 41197..41454 - 258 WP_000759841 EexN family lipoprotein -
HTM42_RS00225 41464..42234 - 771 WP_000716326 type IV secretion system protein -
HTM42_RS00230 42244..44997 - 2754 WP_000108726 VirB3 family type IV secretion system protein virb4
HTM42_RS00235 45022..45312 - 291 WP_000916156 TrbC/VirB2 family protein virB2
HTM42_RS00240 45296..45940 - 645 WP_000953538 lytic transglycosylase domain-containing protein virB1
HTM42_RS00245 45986..46222 - 237 WP_001348696 hypothetical protein -
HTM42_RS00250 46173..46823 - 651 WP_004208545 transcription termination/antitermination NusG family protein -
HTM42_RS00255 47035..48195 - 1161 WP_004199101 MobP1 family relaxase -
HTM42_RS00260 48198..48743 - 546 WP_001348698 DNA distortion polypeptide 1 -
HTM42_RS00265 49084..49341 - 258 WP_004199355 hypothetical protein -
HTM42_RS00270 49338..49490 - 153 WP_162542717 hypothetical protein -
HTM42_RS00275 49577..49915 - 339 WP_001099725 hypothetical protein -
HTM42_RS00280 50009..50251 - 243 WP_000008707 hypothetical protein -
HTM42_RS00285 50241..50522 - 282 WP_001348701 hypothetical protein -

Host bacterium

ID   3579 GenBank   NZ_KY659387
Plasmid name   pCfr-30 Incompatibility group   IncX3
Plasmid size   53292 bp Coordinate of oriT [Strand]   48521..49138 [+]
Host baterium   Citrobacter freundii strain 30

Cargo genes

Drug resistance gene   blaKPC-3, blaSHV-182
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -